16 refactor tests #20

alexgrent · 2025-03-24T08:58:43Z

PR for test refactoring

…ometry + aggregate relationships for composition

# Conflicts: # pom.xml

…changes

…feature/nested-components # Conflicts: # src/main/java/org/reactome/server/graph/domain/model/DatabaseObject.java

…pwb-changes

…-refactor-tests # Conflicts: # src/main/java/org/reactome/server/graph/aop/README.md # src/test/java/org/reactome/server/graph/service/AdvancedServiceTest.java # src/test/java/org/reactome/server/graph/service/DiagramServiceTest.java # src/test/java/org/reactome/server/graph/service/ParticipantServiceTest.java

EliotRagueneau

Quite a few bits to change:

Use static variable as much as possible instead of raw string, specially in code base but also in tests
Avoid breaking logic of tests when refactoring. If you do not understand the difference between 2 tests, or that the logic is completely confusing to you, please ask instead of assuming the tests are just wrong. It might be the case, but it is worth asking in case the logic might actually be relevant, because in most cases it actually is
Make sure to use the ofrmatter from intellij when coding, cmd + opt + L should be a reflex by now

Overall big work and efforts, greatly appreciated, but I think you should have been a bit more patient with some tests and really have tried to understand what was intended to be tested, because you miss the point of quite a few tests, and even deleted some. the aim is of course not to always have all tests green, otherwise you would just have no test at all and problem solved ;)

EliotRagueneau · 2025-03-25T11:56:40Z

src/main/java/org/reactome/server/graph/aop/README.md

 <img src=https://cloud.githubusercontent.com/assets/6883670/22938783/bbef4474-f2d4-11e6-92a5-07c1a6964491.png width=220 height=100 />

-Aspect-Oriented Programming with Spring
+Aspect Oriented Programming with Spring


that was better before

EliotRagueneau · 2025-03-25T11:56:55Z

src/main/java/org/reactome/server/graph/aop/README.md

 :warning: Changes in this package have to be taken carefully, considering it is going to reflect in the whole application

 ### What is Aspect-Oriented Programming - AOP?



that was better before

EliotRagueneau · 2025-03-25T11:57:03Z

src/main/java/org/reactome/server/graph/aop/README.md

 ### What is Aspect-Oriented Programming - AOP?

-Spring AOP framework is used to modularize cross-cutting concerns in aspects. Simply, it’s just an interceptor to intercept some processes, for example, when a method is executed, Spring AOP can hijack the executing method, and add extra functionality before or after the method execution. The most used feature is logging.
+Spring AOP framework is used to modularize cross-cutting concerns in aspects. Simply, t’s just an interceptor to intercept some processes, for example, when a method is execute, Spring AOP can hijack the executing method, and add extra functionality before or after the method execution. The most used feature is logging.


that was better before

EliotRagueneau · 2025-03-25T14:38:19Z

src/main/java/org/reactome/server/graph/domain/model/Event.java

    }

-    public void setDeletedList(List<Deleted> deleted) {
+    public void setDeleted(List<Deleted> deleted) {


Unsure about this one, need to be tested to be sure it's working

EliotRagueneau · 2025-03-25T14:41:07Z

src/main/java/org/reactome/server/graph/domain/model/Deleted.java

 import org.springframework.data.neo4j.core.schema.Node;
 import org.springframework.data.neo4j.core.schema.Relationship;

+import javax.management.relation.Relation;


Wrong import?

EliotRagueneau · 2025-03-27T17:31:41Z

src/test/java/org/reactome/server/graph/util/ReactionType.java

+package org.reactome.server.graph.util;
+
+public enum ReactionType {
+    ASSOCIATION,DISSOCIATION,TRANSITION, BINDING


formatting pls

EliotRagueneau · 2025-03-27T17:33:04Z

src/test/java/org/reactome/server/graph/util/TestNodeRepository.java

+@Repository
+public class TestNodeRepository {
+
+    private final Neo4jClient neo4jClient;


Please add //language=Cypher before queries

EliotRagueneau · 2025-03-27T17:34:50Z

src/test/java/org/reactome/server/graph/service/SpeciesServiceTest.java

    @Test
    public void testGetSpeciesAnyId(){
-        Species species = speciesService.getSpecies(9606);
+        Species species = speciesService.getSpecies(testSpecies.getDbId());


EliotRagueneau · 2025-03-27T17:38:53Z

src/test/java/org/reactome/server/graph/service/StabilityAndConsistencyTest.java

    @SuppressWarnings("Duplicates")
    @Test
-    public void libraryStabilityTest() {
+    public void libraryStabilityTest() {  // This test makes no sense


I agree, I think there is made because sometimes, when we queried twice for the same thing with another query in the middle, then the second one wasn't the same. This is ensuring this is not the case with the current library version we are using of SDN. Please keep something similar

EliotRagueneau · 2025-03-27T17:41:31Z

src/test/java/org/reactome/server/graph/service/StabilityAndConsistencyTest.java

    }

    @Test
    public void lazyLoadingStoichiometryTest(){


This is to test that you get the same result by lazy loading a property, and by directly querying for it. It also checks that the stoichiometry expansion works in both cases. Please reintegrate similar test

cqgong and others added 30 commits April 5, 2024 14:40

✨ introduce the molecule type for re when it's used as an interior

f12af5c

🚚 Move reactome-pwp repos to reactome organisation

93a926d

Merge remote-tracking branch 'origin/dev' into dev

23c3467

🔊 Make logs use maven properties properly

0f875fc

✨ Support bounded physical entity subunits

ea366f7

♻️ Support additional views where relationships have explicit stoichi…

fa72c48

…ometry + aggregate relationships for composition

✅ Update some tests

7703a31

🐛 Ignore new fake fields from ReactomeSchema

84d9f87

🐛 Fix Class cast issue with getComposedOf

d4bc5e3

🗃️ Include refs in enhanced cypher query

ff1c5e6

Merge branch 'feature/add-molecule-type' into feature/new-pwb-changes

551c88f

# Conflicts: # pom.xml

🗃️ Include authors from publication

f815654

Merge branch 'feature/enhanced-query-with-refs' into feature/new-pwb-…

fe64f74

…changes

Ref. tests

cee8703

♿ Access person info for instanceEdit

aba7513

Test Ref test DB

9572242

Merge remote-tracking branch 'origin/feature/nested-components' into …

2f27db7

…feature/nested-components # Conflicts: # src/main/java/org/reactome/server/graph/domain/model/DatabaseObject.java

Merge branch 'refs/heads/feature/nested-components' into feature/new-…

65bba7e

…pwb-changes

✨ Add diseasePathways

135f2b5

Advanced linkage service mock ref

db119dd

✨ Support enhancedQuery for drugs end chemicals

9214fc0

Test Refactoring

6e5f01b

Test Ref CompartmentTest

8e676f5

Test Ref Database object

a608cd2

Test Ref Database with ID

ecb2930

Test Ref DeletedInstanceServiceTest

c8ec339

Test Ref Delted service test

5069811

TR Diagram service Test

9e0f8a0

TR DOI test

8e7a754

TR Events service Test, change Basetests top level pathway

c99d424

alexgrent added 26 commits February 24, 2025 13:31

test ref species service

cfa78cb

test ref update tracker

df55a49

test ref bug Physical Entity

aa5f991

test StabilityAndConsistencyTest

af8b22c

bug MappingService

cd08eb9

bug InteractionTest

cb4a920

bug SpeciesServiceTest

cde77c9

bug db version

94e1944

GKinstance test

7732ca8

test ref

c5bec12

test ref BUG fix

139ae25

test hysical entity bug fix

3305d00

test add ewas data

e6a1e4d

test ref

92d81b3

test ref

2c2b849

Ref Tests

ce3b3d1

Location pathway browser

80d8ece

bug test

21341b2

bug test

c970a2b

Relationship refactoring

756d447

base test

2baf75e

add modifcation Enum

f2ec762

enum reacitonType

9948241

base test

3fde312

hierachy test

6f4e2a0

alexgrent requested a review from EliotRagueneau March 24, 2025 08:58

alexgrent self-assigned this Mar 24, 2025

alexgrent linked an issue Mar 24, 2025 that may be closed by this pull request

Refactor Tests #16

Open

EliotRagueneau requested changes Mar 27, 2025

View reviewed changes

		:warning: Changes in this package have to be taken carefully, considering it is going to reflect in the whole application

		### What is Aspect-Oriented Programming - AOP?

16 refactor tests #20

Are you sure you want to change the base?

16 refactor tests #20

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alexgrent commented Mar 24, 2025

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